From patenting genes to proteins: the search for utility via function

The debate regarding the patenting of genes has extended into the post-genome era. With only approximately 35000 genes deduced from the draft sequence of the human genome, there are fears that a few companies have already gained monopoly on the potential benefits from this knowledge. Nevertheless, it is accepted that proteins determine gene function and function is not readily predicted from gene sequence. Furthermore, genes can encode multiple proteins and a single protein can have multiple functions. Here, we argue that unraveling the intrinsic complexity of proteins and their functions is the key towards determining the utility requirement for patenting protein inventions and consider the possible socioeconomic impact.     

Ion channels in plants: From bioelectricity,via signaling,to behavioral actions

In his recent opus magnum review paper published in the October issue of Physiology Reviews, Rainer Hedrich summarized the field of plant ion channels.¹ He started from the earliest electric recordings initiated by Charles Darwin of carnivorous Dionaea muscipula,^1,2 known as Venus flytrap, and covered the topic extensively up to the most recent discoveries on Shaker-type potassium channels, anion channels of SLAC/SLAH families, and ligand-activated channels of glutamate receptor-like type (GLR) and cyclic nucleotide-gated channels (CNGC).¹     

Lateral meristems of higher plants: Phytohormonal and genetic control

Lateral meristems (pericycle, procambium and cambium, phellogen) are positioned in parallel to the lateral surface of the organ, where they are present, and produce concentric layers of undifferentiated cells. Primary lateral meristems, procambium and pericycle, arise during embryogenesis; secondary lateral meristems, cambium and phellogen, — during post embryonic development. Pericycle is most pluripotent plant meristem, as it may give rise to a variety of other types of meristems: lateral meristems (cambium, phellogen), apical meristems of lateral roots, and also shoot meristems during plant in vitro regeneration. Procambium and cambium developing from it give rise to the vascular tissues of the stems and roots, ensuring their thickening. The review considers the genetic control of lateral meristem development and the role of phytohormones in the control of their activities.     

Regeneration of whole plants from apical meristems of Pinus radiata

A methodology to regenerate whole plants of Pinus radiata from apical meristems of 3- and 7-year-old trees was developed. Meristematic domes with two or three leaf primordia were excised from surface-sterilized branch tips of field-grown plants and cultured in LP medium with half strength macronutrients (1/2 LP) and full strength micronutrients. The early growth of meristems required approximately 12 weeks, including a recovery stage during the first 2 weeks. After 8 weeks, some meristems developed abnormal phenotypes and died during the subsequent stages of development. However, healthy meristems elongated and formed shoots when they were transferred to LP medium supplemented with MS vitamins, 30 mg l^–1 casein hydrolysate, and 0.4 g l^–1 agar plus 2.85 g l^–1 Gelrite. Meristems that developed vigorous shoots were used for rooting experiments when they were 2 cm in length. Whole plants were obtained after 5 days of root induction in water-agar medium containing 8.2 M IBA and 5.4 M NAA and 1 month culture in LP medium with 10 g l^–1 sucrose. Plants regenerated from meristems were further propagated by rooting of cuttings. Of the rooted cuttings, 10% were morphologically juvenile.     

The significance of apical meristems in the phylogeny of land plants

Two principal types of shoot apex are recognized, (1) the classical pyramidal apical cell of pteridophytes which does not divide periclinally, and so never contributes directly to the inner tissues of the axis, and (2) that of seed plants, in which there are one or more superposed initials of which the innermost contributes directly to inner tissues by periclinal divisions. The occurrence of these types in the major groups of living land plants is reviewed. The first type is present in ferns,Equisetum, Psilotum, Tmesipteris, Selaginella, and bryophytes (when apical growth occurs in them). The second type occurs in all angiosperms and gymnosperms, and also inLycopodium, Phylloglossum, Isoetes, andStylites. No exceptions nor intermediate conditions occur. Both types of apex are known in Carboniferous fossils, the first type in sphenopsids and the second in pteridosperms and cordaitean gymnosperms. These apices define two evolutionary lines of land plants which may have originated separately as sporophytes from ancestors with no diploid generation. Correlation of these types with the following features is considered: sieve-element inclusions; initiation of leaves and sporangia; the primary vascular system; embryogeny, the vascular cambium; initiation of lateral roots and the type of branching. Seed plants and pteropsids differ in respect of all these features, giving support to the hypothesis that the sporophytes of these two groups arose independently. The position of sphenopsids and lycopsids is also considered.     

KNOX homeobox genes potentially have similar function in both diploid unicellular and multicellular meristems, but not in haploid meristems

Members of the class 1 knotted-like homeobox (KNOX) gene family are important regulators of shoot apical meristem development in angiosperms. To determine whether they function similarly in seedless plants, three KNOX genes (two class 1 genes and one class 2 gene) from the fern Ceratopteris richardii were characterized. Expression of both class 1 genes was detected in the shoot apical cell, leaf primordia, marginal part of the leaves, and vascular bundles by in situ hybridization, a pattern that closely resembles that of class 1 KNOX genes in angiosperms with compound leaves. The fern class 2 gene was expressed in all sporophyte tissues examined, which is characteristic of class 2 gene expression in angiosperms. All three CRKNOX genes were not detected in gametophyte tissues by RNA gel blot analysis. Arabidopsis plants overexpressing the fern class 1 genes resembled plants that overexpress seed plant class 1 KNOX genes in leaf morphology. Ectopic expression of the class 2 gene in Arabidopsis did not result in any unusual phenotypes. Taken together with phylogenetic analysis, our results suggest that (a) the class 1 and 2 KNOX genes diverged prior to the divergence of fern and seed plant lineages, (b) the class 1 KNOX genes function similarly in seed plant and fern sporophyte meristem development despite their differences in structure, (c) KNOX gene expression is not required for the development of the fern gametophyte, and (d) the sporophyte and gametophyte meristems of ferns are not regulated by the same developmental mechanisms at the molecular level.     

From estrogens via alkaloids to enzymes

This personal and professional autobiography covers the 57-year period from 1948 to 2005 and includes the studies at the Faculty of Chemical Technology of the Slovak Technical University and the Faculty of Pharmacy of Comenius University, both in Bratislava, as well as the activities at the Regional Pharmaceutical Research Institute and the Institute of Chemistry of the Slovak Academy of Sciences in Bratislava, the Institute of Organic Chemistry and Biochemistry in Prague, Karolinska Institutet in Stockholm and at other research and scientific working places in Slovakia and abroad. It highlights the research on natural substances and enzymes, especially the pectin methyl esterase.     

Comparative analysis of expressed genes from cacao meristems infected by Moniliophthora perniciosa

BACKGROUND AND AIMS: Witches' broom disease is caused by the hemibiotrophic basidiomycete Moniliophthora perniciosa, and is one of the most important diseases of cacao in the western hemisphere. Because very little is known about the global process of such disease development, expressed sequence tags (ESTs) were used to identify genes expressed during the Theobroma cacao-Moniliophthora perniciosa interaction. METHODS: Two cDNA libraries corresponding to the resistant (RT) and susceptible (SP) cacao-M. perniciosa interactions were constructed from total RNA, using the DB SMART Creator cDNA library kit (Clontech). Clones were randomly selected, sequenced from the 5' end and analysed using bioinformatics tools including in silico analysis of the differential gene expression. KEY RESULTS: A total of 6884 ESTs were generated from the RT and SP cDNA libraries. These ESTs were composed of 2585 singlets and 341 contigs for a total of 2926 non-redundant sequences. The redundancy of the libraries was low and their specificity high when compared with the few other cacao libraries already published. Sequence analysis allowed the assignment of a putative functional category for 54 % of sequences, whereas approx. 22 % of sequences corresponded to unknown function and approx. 24 % of sequences did not show any significant similarity with other proteins present in the database. Despite the similar overall distribution of the sequences in functional categories between the two libraries, qualitative differences were observed. Genes involved during the defence response to pathogen infection or in programmed cell death were identified, such as pathogenesis related-proteins, trypsin inhibitor or oxalate oxidase, and some of them showed an in silico differential expression between the resistant and the susceptible interactions. CONCLUSIONS: As far as is known this is the first EST resource from the cacao-M. perniciosa interaction and it is believed that it will provide a significant contribution to the understanding of the molecular mechanisms of the resistance and susceptibility of cacao to M. perniciosa, to develop strategies to control witches' broom, and as a source of polymorphism for molecular marker development and marker-assisted selection.     

Dissecting the sterol C-4 demethylation process in higher plants. From structures and genes to catalytic mechanism

Sterols become functional only after removal of the two methyl groups at C-4. This review focuses on the sterol C-4 demethylation process in higher plants. An intriguing aspect in the removal of the two C-4 methyl groups of sterol precursors in plants is that it does not occur consecutively as it does in yeast and animals, but is interrupted by several enzymatic steps. Each C-4 demethylation step involves the sequential participation of three individual enzymatic reactions including a sterol methyl oxidase (SMO), a 3β-hydroxysteroid-dehydrogenase/C4-decarboxylase (3βHSD/D) and a 3-ketosteroid reductase (SR). The distant location of the two C-4 demethylations in the sterol pathway requires distinct SMOs with respective substrate specificity. Combination of genetic and molecular enzymological approaches allowed a thorough identification and functional characterization of two distinct families of SMOs genes and two 3βHSD/D genes. For the latter, these studies provided the first molecularly and functionally characterized HSDs from a short chain dehydrogenase/reductase family in plants, and the first data on 3-D molecular interactions of an enzyme of the postoxidosqualene cyclase sterol biosynthetic pathway with its substrate in animals, yeast and higher plants. Characterization of these three new components involved in C-4 demethylation participates to the completion of the molecular inventory of sterol synthesis in higher plants.     

From nuclear genes to chloroplast localized proteins

There is broad evidence that an endosymbiotic uptake of a cyanobacterial-type organism was the point of origin for the evolution of chloroplasts. During organelle evolution extensive gene transfer from the symbiont to the host genome occurred, which raises the question of how these gene products, namely proteins, which are still functional in chloroplasts, find their way back ‘home’. Nuclear-encoded proteins enter plastids via a complex import machinery that requires the coordinate interplay of a variety of soluble and membrane-bound factors on the cytosolic site as well as on the stromal side of the chloroplast envelope membranes. We define that the process called ‘import of chloroplast precursor proteins’ begins with the release of the polypeptide from the ribosomes and binding to cytosolic factors, such as a guidance complex, which accompanies (chaperones) proteins to chloroplasts. The translocation across the envelope membranes engages distinct translocation machineries at the outer and the inner envelope membranes. Additionally subsequent sorting events to different subcompartments within the plastids are operated by a number of distinct pathways, all of which seem to involve multiple subunits, which are largely of bacterial (symbiotic) origin. The evolutionary history of proteins mediating the import of chloroplast constituents across the envelope membranes seems more diverse. Since cyanobacteria lack a protein import pathway, it is not surprising that only a few subunits of the chloroplast translocon seem to be of symbiotic origin while others seem to be eukaryotic additions.